Background Abnormalities of the ventral lamina of the sixth cervical vertebra (AVL-C6) are thought to exert abnormal stress on the articular process joints (APJs) of the cervicothoracic junction. The aim of the study was to investigate the association between AVL-C6 and radiographic findings in the caudal cervical area and between clinical signs of neck pain and ataxia and radiographic findings. Methods Medical records of horses subjected to cervical radiography were reviewed. Horses were classified into those with neck pain (group C), those with ataxia (group A) and healthy horses (group H). Presence of AVL-C6 and increased size, dysplasia, remodelling, fragmentation and osteochondral fragment at the APJs (C5–T1) were recorded. Univariable logistic regression analysis was performed to identify the associations between explanatory and dependent variables. Variables with P<0.2 were included in the multivariable analysis. Results One hundred and sixteen horses were included (44 in group C, 29 in group A, 66 in group H); 24 of 116 horses had radiographic AVL-C6. Age, AVL-C6 and overall/C6–C7 increase in size remained in the final models. Conclusions The presence of AVL-C6 and moderate/severe increase in size of the caudal cervical APJs increase the odds of showing neck pain and, if severe, ataxia.